Evolution of Spatial and Temporal cis-Regulatory Divergence in Sticklebacks

Area of Science:

• Evolutionary biology
• Genomics
• Developmental biology

Background:

• Cis-regulatory changes are crucial for adaptation.
• Threespine sticklebacks exhibit rapid adaptation to freshwater environments.
• Understanding gene regulatory evolution is key to explaining adaptive divergence.

Purpose of the Study:

• Investigate cis-regulatory changes in gene expression between marine and freshwater stickleback ecotypes.
• Characterize tissue-specific and developmental cis-regulatory divergence.
• Identify genomic regions under selection related to cis-regulatory changes.

Main Methods:

• Analyzed allele-specific expression (ASE) in F1 hybrids of marine and freshwater sticklebacks.
• Surveyed seven ecologically relevant tissues across two developmental stages.
• Applied genome-wide tests for selection on cis-regulatory changes.

Main Results:

• Identified cis-regulatory divergence affecting one-third of genes, with nearly half being tissue-specific.
• Found lineage-specific selection on processes like the Wnt signaling pathway in dental tissues.
• Observed enrichment of genes with ASE in regions of repeated marine-freshwater divergence.

Conclusions:

• Tissue-specific cis-regulatory changes play a fundamental role in the rapid adaptation of sticklebacks to freshwater.
• These regulatory differences contribute to parallel adaptive evolution across distinct populations.
• The study provides insights into the cis-regulatory landscape driving ecotype divergence.